rs357758

chr2-71138150-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005791.3(MPHOSPH10):c.1099-340C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,128 control chromosomes in the GnomAD database, including 6,100 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (6100 hom., cov: 33)
• Consequence: MPHOSPH10 NM_005791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

MPHOSPH10 (HGNC:7213): (M-phase phosphoprotein 10) This gene encodes a protein that is phosphorylated during mitosis. The protein localizes to the nucleolus during interphase and to the chromosomes during M phase. The protein associates with the U3 small nucleolar ribonucleoprotein 60-80S complexes and may be involved in pre-rRNA processing. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MPHOSPH10	NM_005791.3	c.1099-340C>T		intron_variant		ENST00000244230.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPHOSPH10	ENST00000244230.7	c.1099-340C>T		intron_variant		1	NM_005791.3	P1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41808 AN: 152010 Hom.: 6101 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.283

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.275 AC: 41830 AN: 152128 Hom.: 6100 Cov.: 33 AF XY: 0.276 AC XY: 20537 AN XY: 74374

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.280

Alfa AF: 0.303 Hom.: 11144

Bravo AF: 0.281

Asia WGS AF: 0.285 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.22
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs357758; hg19: chr2-71365280;